Folding, regional

The second type of quantum monodromy occurs in the computed bending-vibrational bands of LiCN/LiNC, in which the role of the isolated critical point is replaced by that of a finite folded region of the spectrum, where the vibrational states of the secondary isomer LiNC interpenetrate those of LiCN [9, 10]. The folded region is finite in this case, because the secondary minimum on the potential surface merges with the transition state as the angular momentum increases. However, the shape of the potential energy surface in HCN prevents any such angular momentum cut-off, so monodromy is forbidden [10]. 

Limited proteolysis. Flexible regions of proteins can sometimes be removed by digestion of the protein with different proteases. This technique is based on the techniques that were used to determine the core folded regions of proteins, most notably antibodies (Porter, 1973). Limited proteolysis can be used to remove flexible loops of proteins, or separate multidomain proteins into separate domains and has been used successfully in a number of instances (Noel et al., 1993 Sondek et al., 1996 Mazza et al., 2002). 

All three of the classical mechanisms of folding (Figure 19.1) are ruled out by these observations, as is the jigsaw model. The framework and nucleation models imply that there are fully formed elements of secondary structure in the transition state of folding. Regions within the classical nucleus or the preformed... 

This scheme can also accommodate the synthesis of membrane-bound proteins. In this case, the protein is not released into the lumen of the ER, but rather stays bound to the membrane. One or more anchor sequences (or stop-transfer sequences ) in the newly made protein keeps the partially folded region of the protein in the membrane. 

A domain is an independently folded region of a protein e.g., the NAD+-binding domain of glyceraldehyde-3-phosphate dehydrogenase. 

Independent folding regions within a protein. The group/pattern of secondary structures forming a Domain s tertiary structure is called a Fold. (Characteristic bond type hydrophobic others hydrogen, ion-pair, van der Waals.)... 

Large proteins often contain distinct domains, independently folded regions of tertiary structure with characteristic structural or functional properties or both (see Figure 3-7). 

Domain 3 stretches from amino acids 463 (432) to 645 (589) and corresponds to exons 5, 6, and 7. The core of domain 3 is again a single a-helix stabilized by intrahelix salt bridges. The sequence from 565 (509) to 621 (565) is 43% identical to the amino acids 90-146 of rabbit skeletal muscle troponin T, which is a TM binding site in troponin T. Domain 4 stretches from 646 (590) to the C terminus and corresponds to exons 8-13. This is an extended and stably folded region that contains little regular secondary structure (Levine et al.,... 

Not all of the fibroin protein is in / -sheets. As the amino acid composition in Figure 6.12 shows, fibroin contains small amounts of other, bulky amino acids like valine and tyrosine, which would not fit into the structure shown. These are carried in compact folded regions that periodically interrupt the sheet segments, and they probably account for the amount of stretchiness that silk fibers have. In fact, different species of silkworms produce fibroins with different extents of such non - / -sheet structure and corresponding differences in elasticity. The overall fibroin structure is a beautiful example of a protein molecule that has evolved to perform a particular function — to provide a tough, yet flexible fiber for the silkworm s cocoon or the spider s web. 

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